Search for: All records

Abstract BackgroundVariation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to minimize the variation among biological replicates. ResultsWe demonstrate that the common statistics relative standard deviation (RSD) and coefficient of variation (CV), which are often used for quality control or part of a larger pipeline in omics analyses, can also be used as a metric of a physiological stress response. Using an approach we term Replicate Variation Analysis (RVA), we demonstrate that acute physiological stress leads to feature-wide canalization of CV profiles of metabolomes and proteomes across biological replicates. Canalization is the repression of variation between replicates, which increases phenotypic similarity. Multiple in-house mass spectrometry omics datasets in addition to publicly available data were analyzed to assess changes in CV profiles in plants, animals, and microorganisms. In addition, proteomics data sets were evaluated utilizing RVA to identify functionality of reduced CV proteins. ConclusionsRVA provides a foundation for understanding omics level shifts that occur in response to cellular stress. This approach to data analysis helps characterize stress response and recovery, and could be deployed to detect populations under stress, monitor health status, and conduct environmental monitoring. 

Abstract Regression test selection (RTS) approaches reduce the cost of regression testing of evolving software systems. Existing RTS approaches based on UML models use behavioral diagrams or a combination of structural and behavioral diagrams. However, in practice, behavioral diagrams are incomplete or not used. In previous work, we proposed a fuzzy logic based RTS approach called FLiRTS that uses UML sequence and activity diagrams. In this work, we introduce FLiRTS 2, which drops the need for behavioral diagrams and relies on system models that only use UML class diagrams, which are the most widely used UML diagrams in practice. FLiRTS 2 addresses the unavailability of behavioral diagrams by classifying test cases using fuzzy logic after analyzing the information commonly provided in class diagrams. We evaluated FLiRTS 2 on UML class diagrams extracted from 3331 revisions of 13 open-source software systems, and compared the results with those of code-based dynamic (Ekstazi) and static (STARTS) RTS approaches. The average test suite reduction using FLiRTS 2 was 82.06%. The average safety violations of FLiRTS 2 with respect to Ekstazi and STARTS were 18.88% and 16.53%, respectively. FLiRTS 2 selected on average about 82% of the test cases that were selected by Ekstazi and STARTS. The average precision violations of FLiRTS 2 with respect to Ekstazi and STARTS were 13.27% and 9.01%, respectively. The average mutation score of the full test suites was 18.90%; the standard deviation of the reduced test suites from the average deviation of the mutation score for each subject was 1.78% for FLiRTS 2, 1.11% for Ekstazi, and 1.43% for STARTS. Our experiment demonstrated that the performance of FLiRTS 2 is close to the state-of-art tools for code-based RTS but requires less information and performs the selection in less time. 

ABSTRACT We describe the discovery of an archaeal virus, one that infects archaea, tentatively named Thermoproteus spherical piliferous virus 1 (TSPV1), which was purified from a Thermoproteales host isolated from a hot spring in Yellowstone National Park (USA). TSPV1 packages an 18.65-kb linear double-stranded DNA (dsDNA) genome with 31 open reading frames (ORFs), whose predicted gene products show little homology to proteins with known functions. A comparison of virus particle morphologies and gene content demonstrates that TSPV1 is a new member of the Globuloviridae family of archaeal viruses. However, unlike other Globuloviridae members, TSPV1 has numerous highly unusual filaments decorating its surface, which can extend hundreds of micrometers from the virion. To our knowledge, similar filaments have not been observed in any other archaeal virus. The filaments are remarkably stable, remaining intact across a broad range of temperature and pH values, and they are resistant to chemical denaturation and proteolysis. A major component of the filaments is a glycosylated 35-kDa TSPV1 protein (TSPV1 GP24). The filament protein lacks detectable homology to structurally or functionally characterized proteins. We propose, given the low host cell densities of hot spring environments, that the TSPV1 filaments serve to increase the probability of virus attachment and entry into host cells. IMPORTANCE High-temperature environments have proven to be an important source for the discovery of new archaeal viruses with unusual particle morphologies and gene content. Our isolation of Thermoproteus spherical piliferous virus 1 (TSPV1), with numerous filaments extending from the virion surface, expands our understanding of viral diversity and provides new insight into viral replication in high-temperature environments.